Autophagy is a central cellular mechanism for elimination of damaged proteins, protein complexes, and organelles. This conserved process plays crucial roles in the cellular response to nutrient deprivation and other stresses, in addition to being required for proper cellular and tissue homeostasis during embryonic development and in defense against pathogens. Defects in autophagy pathways are associated with certain human pathologies, including infectious diseases, neurodegenerative disorders, and cancer. In spite of these highly conserved fundamental cellular functions, the molecular and biochemical details of how autophagy is initiated for different cargoes, and the coordination of steps starting from autophagosome initiation to ultimate fusion with the lysosome remain poorly understood.
Pioneering studies in budding yeast first defined 36 core autophagy (“ATG”) genes required for this process, most of which are conserved with mammals. One of the most upstream components of the pathway in yeast is the Atg1 gene, which is notable for being the only core ATG gene to encode a serine/threonine kinase. Atg1 forms a complex with multiple regulatory subunits, including Atg13 and Atg17. In mammals, there appear to be two Atg1 homologs, ULK1 (unc-51 like kinase 1) and ULK2, which similarly bind to an Atg13 homolog and an Atg17 like protein, FIP200. The ULK1 kinase complex is activated in response to nutrient deprivation and is thought to serve as a critical initiator of starvation-induced autophagy. Whether the ULK1 complex is needed for bulk steady-state autophagy that some cell types undergo remains unclear, as well as whether certain forms of selective autophagy may also proceed without involvement of the ULK1 complex. In the context of starvation induced autophagy, ULK1 receives inputs from the cellular energy sensor AMP-activated protein kinase (AMPK), which is activated following cellular stresses that lower intracellular ATP levels, including glucose or oxygen deprivation as well as following mitochondrial insults. Another critical input to ULK1 is the mechanistic target of rapamycin complex 1 (mTORC1). Some nutrient stresses such as amino acid withdrawal do not result in acute AMPK activation, but do trigger rapid mTORC1 inactivation, thereby resulting in ULK1 activation even without the stimulatory input from AMPK. ULK1 is directly phosphorylated on at least one serine, Ser757, by mTORC1, and is phosphorylated on at least four different serines by AMPK to activate it. As most of the aforementioned stresses result in both AMPK activation and mTOR inhibition, starvation should result in an increase in phosphorylation of the AMPK sites in ULK1 and loss of the mTORC1 site. In addition, a recent study suggests that AMPK may directly phosphorylate both Beclin-1 and Vps34, the two central components of the Vps34/Beclin complex which is responsible for localized PI3P production required for autophagosome biogenesis, thus positively mediating autophagic flux. The relative requirements for AMPK phosphorylation of components of the Beclin complex versus phosphorylation the Ulk1 complex in various forms of autophagy remains to be investigated.
There is a need in the art for novel compounds that inhibit ULK1 and can be used to treat ULK1-associated diseases or disorders. The present invention addresses this need.